Phylogenetic analysis and genetic similarities of <i>Phyllidia</i> spp. by comparing the nucleotide sequence of 16S rRNA and cytochrome c genes

Alqudah, A. A.

doi:10.1590/1519-6984.272732

Acessibilidade / Reportar erro

Brasil

Brazilian Journal of Biology

Español English

Brasil

Español English

sumário « anterior atual seguinte »

Sumário

Original Article • Braz. J. Biol. 84 • 2024 • https://doi.org/10.1590/1519-6984.272732 copy

Phylogenetic analysis and genetic similarities of Phyllidia spp. by comparing the nucleotide sequence of 16S rRNA and cytochrome c genes

Análise filogenética e similaridades genéticas de Phyllidia spp. comparadas à sequência de nucleotídeos dos genes 16S rRNA e citocromo c

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Phyllidiid nudibranchs are brightly colored gastropod molluscs, frequently encountered in coral reefs of the tropical Indo-Pacific. This study aimed to identify the phylogenetic similarities among the Phyllidia spp. The phylogenetic similarities among all the available Phyllidia spp. were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome c genes (cox I). Sequences were retrieved from NCBI databases and aligned by using Geneious software. A phylogenetic tree was constructed for the retrieved sequences of Phyllidia spp. by using the neighbor-joining method on MEGA software and the pairwise distances were also calculated. The similarities among nucleotide sequences of 16s rRNA showed that the P. elegans, and P. haegeli had the highest similarities (99.92%) and the lowest similarities (99.14%) among P. haegeli and P. picta. While nucleotide sequences of cox I showed the highest similarities (99.90%) between P. elegans and P. ocellata, and the P. varicosa had the lowest similarities 99.74% with P. koehleri and P. larryi. The molecular phylogenetic analysis based on mitochondrial marker indicated a close relation between P. elegans and P. alyta in both cox I and 16s rRNA phylogenetic tree. The phylogenetic tree of 16s rRNA gene shows the P. ocellata is closely related to the clade of species P. exquisita. The available phylogenetic analysis could be useful in further studies of Phyllidiidae within Nudibranchia.

Keywords:
nudibranchs; Phyllidia species; 16s rRNA; cytochrome c genes; Geneious software

Species	Accession number	Reference	Collection locality
Phyllidia elegans	MZ964197.1	Papu et al. (2022)	Indonesia
Phyllidia picta	MZ964164.1	Papu et al. (2022)	Indonesia
Phyllidia coelestis	MN690289.1	Yin et al. (2019)	Singapore
Phyllidia ocellata	MZ964254.1	Papu et al. (2022)	Indonesia
Phyllidia alyta	MZ817992.1	Papu et al. (2022)	Indonesia
Phyllidia flava	ON212011.1	Furfaro et al. (2022)FURFARO, G., SCHREIER, C., TRAINITO, E., PONTES, M., MADRENAS, E., GIRARD, P. and MARIOTTINI, P., 2022. The sea slug Doriopsilla areolata Bergh, 1880 (Mollusca, Gastropoda) in the Mediterranean Sea: another case of cryptic diversity. Diversity, vol. 14, no. 4, p. 297. http://dx.doi.org/10.3390/d14040297. http://dx.doi.org/10.3390/d14040297...	Mediterranean Sea
Phyllidia babai	KX235918.1	Stoffels et al. (2016)STOFFELS, B.E.M.W., VAN DER MEIJ, S.E.T., HOEKSEMA, B.W., VAN ALPHEN, J., VAN ALEN, T., MEYERS-MUÑOZ, M.A., DE VOOGD, N.J., TUTI, Y. and VAN DER VELDE, G., 2016. Phylogenetic relationships within the Phyllidiidae (Opisthobranchia, Nudibranchia). ZooKeys, no. 605, pp. 1-35. PMid:27551210.	West Papua
Phyllidia koehleri	OQ206951.1	Cunha et al. (2023)	Maldives
Phyllidia larryi	KP871649.1.	Mahguib and Valdés (2015)	California
Phyllidia exquisite	MZ964208.1	Papu et al. (2022)	Indonesia
Phyllidia varicosa	MZ964306.1	Papu et al. (2022)	Indonesia
Phyllidia haegeli	MZ964205.1	Papu et al. (2022)	Indonesia
Scaphander lignarius.	MN433678.1	Siegwald et al. (2020)SIEGWALD, J., PASTORINO, G., OSKARS, T. and MALAQUIAS, M.A.E., 2020. A new species of the deep-sea genus Scaphander (Gastropoda, Cephalaspidea) from the Mar del Plata submarine canyon off Argentina. Bulletin of Marine Science, vol. 96, no. 1, pp. 111-126. http://dx.doi.org/10.5343/bms.2019.0069. http://dx.doi.org/10.5343/bms.2019.0069...	Argentina

Species	Accession number	Reference	Collection locality
Phyllidia elegans	AF430362.2	Valdés (2003)VALDÉS, Á., 2003. Preliminary molecular phylogeny of the radula-less dorids (Gastropoda: Opisthobranchia), based on 16S mtDNA sequence data. The Journal of Molluscan Studies, vol. 69, no. 1, pp. 75-80. http://dx.doi.org/10.1093/mollus/69.1.75. http://dx.doi.org/10.1093/mollus/69.1.75...	New California
Phyllidia picta	MN217677.1	Ompi et al. (2019)	Indonesia
Phyllidia coelestis	MK852557.1	Ompi et al. (2019)	Indonesia
Phyllidia ocellata	MZ955557.1	Papu et al. (2022)	Indonesia
Phyllidia alyta	MT592804.1	Rajendra et al. (2022)RAJENDRA, S., DIXIT, S., NIGAM, N.K. and SIVAPERUMAN, C., 2022. Status and distribution of opisthobranchs of Great Nicobar Biosphere Reserve, India. In: C. SIVAPERUMAN, D. BANERJEE, B. TRIPATHY and K. CHANDRA, eds. Faunal ecology and conservation of the Great Nicobar Biosphere Reserve. Singapore: Springer, pp. 581-620.	India
Phyllidia flava	Not found^* * No sequence found for P. koehleri and P. flava.	__	__
Phyllidia babai	MZ955514.1	Papu et al. (2022)	Indonesia
Phyllidia koehleri	Not found^*	__	__
Phyllidia larryi	KP871697.1	Mahguib and Valdés (2015)	Balearic Islands
Phyllidia exquisita	MZ955512.1	Papu et al. (2022)	Indonesia
Phyllidia varicosa	MK911031.1	Ompi et al. (2019)	Indonesia
Phyllidia haegeli	MZ955508.1	Papu et al. (2022)	Indonesia
Scaphander lignarius.	KJ845728.1	Masi et al. (2015)MASI, L., ADELFI, M.G., PIGNONE, D. and LARATTA, B., 2015. Identification of Doris verrucosa mollusc via mitochondrial 16S rDNA. Biochemical Systematics and Ecology, vol. 58, pp. 21-29. http://dx.doi.org/10.1016/j.bse.2014.10.009. http://dx.doi.org/10.1016/j.bse.2014.10....	Spain

Percentage identity %
Divergence		1	2	3	4	5	6	7	8	9	10	11
	1		99.92	99.68	99.87	99.91	99.88	99.92	99.85	99.91	99.92	99.93
	2	0.08		99.73	99.86	99.91	99.92	99.98	99.86	99.92	99.93	99.94
	3	0.32	0.27		99.64	99.66	99.67	99.68	99.74	99.67	99.70	99.69
	4	0.13	0.11	0.36		99.88	99.89	99.88	99.87	99.86	99.90	99.89
	5	0.09	0.08	0.34	0.12		99.89	99.92	99.86	99.92	99.92	99.14
	6	0.12	0.08	0.33	0.11	0.11		99.91	99.85	99.92	99.91	99.90
	7	0.08	0.03	0.32	0.12	0.08	0.09		99.86	99.17	99.93	99.93
	8	0.15	0.14	0.26	0.13	0.14	0.15	0.14		99.85	99.86	99.85
	9	0.09	0.08	0.33	0.14	0.08	0.09	1.20	0.15		99.92	99.92
	10	0.08	0.07	0.30	0.10	0.08	0.09	0.07	0.14	0.08		99.94
	11	0.07	0.06	0.31	0.11	0.09	0.10	0.07	0.15	0.08	0.06

Percentage identity %
Divergence		1	2	3	4	5	6	7	8	9	10	11	12	13
	1		99.69	99.71	99.72	99.70	99.73	99.70	99.70	99.70	99.70	99.64	99.69	99.66
	2	0.32		99.85	99.87	99.84	99.90	99.84	99.86	99.90	99.85	99.78	99.89	99.89
	3	0.29	0.15		99.86	99.84	99.87	99.85	99.86	99.82	99.82	99.77	99.83	99.86
	4	0.28	0.13	0.15		99.86	99.88	99.83	99.87	99.85	99.86	99.74	99.84	99.88
	5	0.30	0.16	0.16	0.15		99.87	99.82	99.85	99.85	99.85	99.77	99.84	99.88
	6	0.27	0.10	0.13	0.12	0.13		99.86	99.88	99.88	99.81	99.77	99.88	99.89
	7	0.30	0.16	0.15	0.17	0.18	0.14		99.82	99.82	99.82	99.74	99.82	99.81
	8	0.30	0.14	0.14	0.13	0.15	0.12	0.18		99.86	99.85	99.76	99.84	99.88
	9	0.30	0.10	0.18	0.15	0.15	0.12	0.18	0.14		99.84	99.76	99.95	99.85
	10	0.30	0.15	0.18	0.14	0.15	0.12	0.19	0.15	0.16		99.77	99.83	99.87
	11	0.36	0.22	0.23	0.26	0.23	0.23	0.26	0.24	0.24	0.23		99.75	99.83
	12	0.31	0.11	0.17	0.16	0.16	0.13	0.18	0.16	0.05	0.17	0.25		99.86
	13	0.34	0.11	0.14	0.13	0.12	0.11	0.19	0.12	0.15	0.13	0.17	0.14

Instituto Internacional de Ecologia R. Bento Carlos, 750, 13560-660 São Carlos SP - Brasil, Tel. e Fax: (55 16) 3362-5400 - São Carlos - SP - Brazil
E-mail: bjb@bjb.com.br

Acompanhe os números deste periódico no seu leitor de RSS

[1] *e-mail: ali_quda@yahoo.com